Dataset Information

Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.

ABSTRACT: Using a simple viral genome enrichment approach, we report the de novo assembly of the Akata and Mutu Epstein-Barr virus (EBV) genomes from a single lane of next-generation sequencing (NGS) reads. The Akata and Mutu viral genomes are type I EBV strains of approximately 171 kb in length. Evidence for genome heterogeneity was found for the Akata but not for the Mutu strain. A comparative analysis of Akata with another four completely sequenced EBV strains, B95-8/Raji, AG876, Mutu, and GD1, demonstrated that the Akata strain is most closely related to the GD1 strain and exhibits the greatest divergence from the type II strain, AG876. A global comparison of latent and lytic gene sequences showed that the four latency genes, EBNA2, EBNA3A, EBNA3B, and EBNA3C, are uniquely defining of type I and type II strain differences. Within type I strains, LMP1, the latency gene, is among the most divergent of all EBV genes, with three insertion or deletion loci in its CTAR2 and CTAR3 signaling domains. Analysis of the BHLF1 and LF3 genes showed that the reading frames identified in the B95-8/Raji genome are not conserved in Akata (or Mutu, for BHLF1), suggesting a primarily non-protein-coding function in EBV's life cycle. The Akata and Mutu viral-genome sequences should be a useful resource for homology-based functional prediction and for molecular studies, such as PCR, RNA-seq, recombineering, and transcriptome studies. As an illustration, we identified novel RNA-editing events in ebv-miR-BART6 antisense transcripts using the Akata and Mutu reference genomes.

SUBMITTER: Lin Z

PROVIDER: S-EPMC3554088 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.

Lin Zhen Z Wang Xia X Strong Michael J MJ Concha Monica M Baddoo Melody M Xu Guorong G Baribault Carl C Fewell Claire C Hulme William W Hedges Dale D Taylor Christopher M CM Flemington Erik K EK

Journal of virology 20121114 2

Using a simple viral genome enrichment approach, we report the de novo assembly of the Akata and Mutu Epstein-Barr virus (EBV) genomes from a single lane of next-generation sequencing (NGS) reads. The Akata and Mutu viral genomes are type I EBV strains of approximately 171 kb in length. Evidence for genome heterogeneity was found for the Akata but not for the Mutu strain. A comparative analysis of Akata with another four completely sequenced EBV strains, B95-8/Raji, AG876, Mutu, and GD1, demonst ...[more]

PMID: 23152513

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Project description:The main target cells for Epstein-Barr virus (EBV) infection and persistence are B lymphocytes, although T and NK cells can also become infected. In this paper, we characterize the EBV present in 21 pediatric and adult patients who were treated in France for a range of diseases that involve infection of T or NK cells. Of these 21 cases, 5 pediatric patients (21%) and 11 adult patients (52%) were of Caucasian origin. In about 30% of the cases, some of the EBV genomes contain a large deletion. The deletions are different in every patient but tend to cluster near the BART region of the viral genome. Detailed investigation of a family in which several members have persistent T or NK cell infection by EBV indicates that the virus genome deletions arise or are selected independently in each individual patient. Genome sequence polymorphisms in the EBV in these T or NK cell diseases reflect the geographic origin of the patient and not a distinct type of EBV (the 21 cases studied included examples of both type 1 and type 2 EBV infection). Using virus produced from type 1 or type 2 EBV genomes cloned in bacterial artificial chromosome (BAC) vectors, we demonstrate infection of T cells in cord blood from healthy donors. Our results are consistent with transient infection of some T cells being part of normal asymptomatic infection by EBV in young children. IMPORTANCE EBV contributes to several types of human cancer. Some cancers and nonmalignant lymphoproliferative diseases involving T or NK cells contain EBV. These diseases are relatively frequent in Japan and China and have been shown sometimes to have deletions in the EBV genome in the disease cells. We identify further examples of deletions within the EBV genome associated with T or NK cell diseases, and we provide evidence that the virus genomes with these deletions are most likely selected in the individual cases, rather than being transmitted between people during infection. We demonstrate EBV infection of cord blood T cells by highly characterized, cloned EBV genomes and suggest that transient infection of T cells may be part of normal asymptomatic infection by EBV in young children.

Dataset Information

Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.

Publications

Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.

Similar Datasets

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